How to obtain multiple sequence alignments of genomes of selected vertebrate species?

Question

[kousi31]

Hi all,

I want multiple sequence alignments of few vertebrate species (Human, cow, buffalo, sheep and goats). UCSC browser has MSA for 46 vertebrate species and MSA of 3 or 4 species under individual species. But I don't find the combination I need.

Is it possible to extrat MSA of desired species from 46 vertebrate MSA? Or Is it possible to use the pairwise alignments among different species to produce MSA?

Also UCSC does not have information for buffalo. After producing the MSA for other species is it possible to add buffalo genome to the MSA?

I want to project the multiple sequence alignment to buffalo genome as reference sequence.

Answer 1

[andrew.j.skelton73]

Have you considered trying out Ensembl for this problem? Buffalo (or Bison), are available in the MSA functionalities in Ensembl. Here's a video on how to perform MSA of specific species using Ensembl tools.

[kousi31]

A clear tutorial. I need water buffalo (Bubalus bubalis) and it is not in ensemble too.

[kousi31]

Can you please tell me what would be the RAM requirement, If I attempt to do a pairwise alignment between human and buffalo genome (2.7 GB) using LASTZ?..